2-205086880-G-T

Position:

• chr2-205086880-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302769.2(PARD3B):​c.505-17546G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,054 control chromosomes in the GnomAD database, including 5,635 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5635 hom., cov: 32)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

PARD3B (HGNC:14446): (par-3 family cell polarity regulator beta) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in several processes, including establishment of cell polarity; establishment of centrosome localization; and establishment or maintenance of epithelial cell apical/basal polarity. Located in cell junction. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3B	NM_001302769.2	c.505-17546G>T		intron_variant		ENST00000406610.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3B	ENST00000406610.7	c.505-17546G>T		intron_variant		1	NM_001302769.2	P1
PARD3B	ENST00000349953.7	c.505-17546G>T		intron_variant		1
PARD3B	ENST00000351153.5	c.505-17546G>T		intron_variant		1
PARD3B	ENST00000358768.6	c.505-17546G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37488 AN: 151936 Hom.: 5629 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.247 AC: 37505 AN: 152054 Hom.: 5635 Cov.: 32 AF XY: 0.247 AC XY: 18326 AN XY: 74322

Gnomad4 AFR AF: 0.0725

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.244

Alfa AF: 0.301 Hom.: 8358

Bravo AF: 0.233

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7559302; hg19: chr2-205951603;